source("helper_functions.R")
library(cytokit)
library(ggedit)
library(kableExtra)
library(monocle)
library(patchwork)
library(readxl)
library(readr)
library(R.utils)
library(Seurat)
library(tidyverse)
library(viridis)
sample <- c("joint_pons.seurat")
tables_directory <- "tables"
dir.create(tables_directory, showWarnings = FALSE)
monocle_objects_directory <- "monocle_objects"
dir.create(monocle_objects_directory, showWarnings = FALSE)
input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02"
load(file.path(input_directory, "joint_pons.seurat.Rda"))
seurat <- joint_pons
#For some reasons, there is now seurat@misc$colours and seurat@misc$colours_orig
seurat@misc$colours <- seurat@misc$colours_orig
# Convert cluster numbers to format used in levels(seurat@ident)
selected_clusters <- c(20, 13, 15, 3, 6)
selected_clusters <- paste0("^", selected_clusters, "-")
selected_clusters <- grep(paste(selected_clusters,collapse="|"), levels(seurat@ident), value=TRUE)
# Colour vector is not available in this object for these cluster IDs, so they must be recovered a saved object. seurat@misc$colours and seurat@misc$colours_orig are identical vectors. Bug will be fixed later, according to Selin.
# First, recover corresponding new cluster ID.
load("/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02/palettes_joint.Rda")
seurat@misc$colours <- pal_jp
# Cluster columns also need to be renamed.
seurat@meta.data$cluster <- as.character(seurat@meta.data$cluster_joint)
monocle <- seurat_to_monocle(seurat, selected_clusters)
#monocle <- orderCells(monocle, reverse=TRUE)
colours <- monocle@experimentData@other$colours
p <- plot_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)
p <- p + facet_wrap(~cluster) + theme(legend.position = "none")
show(p)
plot_cell_trajectory(monocle, color_by="Pseudotime", show_branch_points = TRUE)
plot_cell_trajectory(monocle, color_by="State", show_branch_points=TRUE)
p <- plot_complex_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)
diff_test_res_all_genes <- differentialGeneTest(monocle,
fullModelFormulaStr = "~sm.ns(Pseudotime)", cores=12)
sig_gene_names_all_genes <- row.names(subset(diff_test_res_all_genes, qval < 0.1))
plot_pseudotime_heatmap(monocle[sig_gene_names_all_genes,],
cores = 12,
num_clusters=1,
show_rownames = FALSE)
diff_test_res_all_genes <- diff_test_res_all_genes %>% rownames_to_column("gene")
write.table(diff_test_res_all_genes, file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_diff_test_res_all_genes.txt"), sep="\t", quote=FALSE, row.names = FALSE)
input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/blancha/analyses/njabado/single_cell/annotation/animaltfdb3.0"
input_file <- "Mus_musculus_TF.txt"
transcription_factors <- read_tsv(file.path(input_directory, input_file), col_types = cols())
significant_genes_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, qval < 5*10^-5) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))
## Number of significant genes: 5151
significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))
## Number of significant transcription factors: 274
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=3, return_heatmap=TRUE, show_rownames = TRUE)
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)
# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_5_10_minus_5[[2]], file.path("figures", "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6", "diff_test_res_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)
## pdf
## 2
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
ph_res_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[2]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])
transcription_factors_table_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
heatmap_matrix_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_q_value_5_10_minus_5 <- heatmap_matrix_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
| gene | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rora | 2.2655226 | 2.1976372 | 2.1300251 | 2.0626244 | 1.9953746 | 1.9282164 | 1.8610915 | 1.7939432 | 1.7267158 | 1.6593550 | 1.5918075 | 1.5240216 | 1.4559467 | 1.3875337 | 1.3187346 | 1.2495029 | 1.1797935 | 1.1095627 | 1.0387683 | 0.9673693 | 0.8953266 | 0.8226024 | 0.7491605 | 0.6749663 | 0.6000216 | 0.5244968 | 0.4486094 | 0.3725718 | 0.2965908 | 0.2208676 | 0.1455983 | 0.0709731 | -0.0028230 | -0.0756103 | -0.1472145 | -0.2174661 | -0.2862006 | -0.3532582 | -0.4184832 | -0.4817242 | -0.5428335 | -0.6016669 | -0.6580833 | -0.7119441 | -0.7631132 | -0.8114562 | -0.8568401 | -0.8991328 | -0.9382024 | -0.9739171 | -1.0061441 | -1.0347492 | -1.0596114 | -1.0807534 | -1.0982781 | -1.1122840 | -1.1228651 | -1.1301108 | -1.1341066 | -1.1349342 | -1.1326717 | -1.1273941 | -1.1191733 | -1.1080786 | -1.0941767 | -1.0775324 | -1.0582082 | -1.0362650 | -1.0117619 | -0.9847570 | -0.9553071 | -0.9234679 | -0.8892945 | -0.8528415 | -0.8141629 | -0.7733126 | -0.7303444 | -0.6853122 | -0.6382702 | -0.5892729 | -0.5383755 | -0.4856339 | -0.4311047 | -0.3748457 | -0.3169156 | -0.2573744 | -0.1962836 | -0.1337059 | -0.0697059 | -0.0043496 | 0.0622950 | 0.1301582 | 0.1991683 | 0.2692515 | 0.3403318 | 0.4123311 | 0.4851692 | 0.5587634 | 0.6330286 | 0.7078775 |
| Hif3a | 3.0000000 | 3.0000000 | 2.9336435 | 2.6986453 | 2.4776628 | 2.2702153 | 2.0757922 | 1.8938623 | 1.7238819 | 1.5653023 | 1.4175756 | 1.2801608 | 1.1525278 | 1.0341617 | 0.9245657 | 0.8232639 | 0.7298032 | 0.6437549 | 0.5647163 | 0.4923111 | 0.4261906 | 0.3660339 | 0.3115483 | 0.2624699 | 0.2185153 | 0.1792038 | 0.1440418 | 0.1125895 | 0.0844536 | 0.0592799 | 0.0367478 | 0.0165649 | -0.0015370 | -0.0178060 | -0.0324726 | -0.0457533 | -0.0578520 | -0.0689625 | -0.0792700 | -0.0889519 | -0.0981797 | -0.1071188 | -0.1159298 | -0.1247683 | -0.1337850 | -0.1431259 | -0.1529316 | -0.1633370 | -0.1744705 | -0.1864533 | -0.1993982 | -0.2134088 | -0.2285682 | -0.2448497 | -0.2621653 | -0.2804255 | -0.2995401 | -0.3194188 | -0.3399725 | -0.3611127 | -0.3827530 | -0.4048088 | -0.4271983 | -0.4498425 | -0.4726653 | -0.4955945 | -0.5185611 | -0.5415003 | -0.5643511 | -0.5870564 | -0.6095635 | -0.6318236 | -0.6537921 | -0.6754284 | -0.6966960 | -0.7175624 | -0.7379985 | -0.7579794 | -0.7774834 | -0.7964921 | -0.8149906 | -0.8329668 | -0.8504115 | -0.8673183 | -0.8836829 | -0.8995038 | -0.9147811 | -0.9295173 | -0.9437163 | -0.9573838 | -0.9705267 | -0.9831534 | -0.9952731 | -1.0068963 | -1.0180341 | -1.0286983 | -1.0389015 | -1.0486564 | -1.0579765 | -1.0668751 |
| Ppara | 2.7908849 | 2.6361951 | 2.4865194 | 2.3419331 | 2.2024874 | 2.0682113 | 1.9391147 | 1.8151896 | 1.6964129 | 1.5827483 | 1.4741479 | 1.3705544 | 1.2719029 | 1.1781222 | 1.0891367 | 1.0048678 | 0.9252352 | 0.8501580 | 0.7795566 | 0.7133531 | 0.6514729 | 0.5938455 | 0.5404057 | 0.4910944 | 0.4458174 | 0.4042874 | 0.3661794 | 0.3311921 | 0.2990457 | 0.2694788 | 0.2422467 | 0.2171188 | 0.1938772 | 0.1723149 | 0.1522347 | 0.1334477 | 0.1157724 | 0.0990342 | 0.0830639 | 0.0676978 | 0.0527767 | 0.0381460 | 0.0236551 | 0.0091574 | -0.0054898 | -0.0204253 | -0.0357835 | -0.0516947 | -0.0682844 | -0.0856731 | -0.1039756 | -0.1233010 | -0.1437416 | -0.1652873 | -0.1878703 | -0.2114219 | -0.2358735 | -0.2611563 | -0.2872023 | -0.3139440 | -0.3413145 | -0.3692484 | -0.3976811 | -0.4265498 | -0.4557928 | -0.4853505 | -0.5151649 | -0.5451798 | -0.5753414 | -0.6055975 | -0.6358985 | -0.6661965 | -0.6964464 | -0.7266050 | -0.7566313 | -0.7864870 | -0.8161357 | -0.8455435 | -0.8746787 | -0.9035116 | -0.9320150 | -0.9601637 | -0.9879346 | -1.0153065 | -1.0422604 | -1.0687791 | -1.0948472 | -1.1204511 | -1.1455790 | -1.1702206 | -1.1943671 | -1.2180115 | -1.2411477 | -1.2637715 | -1.2858795 | -1.3074696 | -1.3285410 | -1.3490936 | -1.3691285 | -1.3886477 |
| Dbp | 2.2506833 | 2.1891815 | 2.1281030 | 2.0673983 | 2.0070196 | 1.9469207 | 1.8870565 | 1.8273835 | 1.7678598 | 1.7084447 | 1.6490989 | 1.5897846 | 1.5304656 | 1.4711068 | 1.4116749 | 1.3521377 | 1.2924647 | 1.2326267 | 1.1725962 | 1.1123470 | 1.0518544 | 0.9910954 | 0.9300483 | 0.8686932 | 0.8070328 | 0.7451737 | 0.6832502 | 0.6213917 | 0.5597230 | 0.4983641 | 0.4374302 | 0.3770316 | 0.3172743 | 0.2582593 | 0.2000835 | 0.1428392 | 0.0866146 | 0.0314940 | -0.0224424 | -0.0751179 | -0.1264593 | -0.1763968 | -0.2248633 | -0.2717947 | -0.3171295 | -0.3608083 | -0.4027738 | -0.4429703 | -0.4813437 | -0.5178410 | -0.5524101 | -0.5849992 | -0.6155648 | -0.6441384 | -0.6707923 | -0.6955962 | -0.7186165 | -0.7399168 | -0.7595578 | -0.7775980 | -0.7940931 | -0.8090970 | -0.8226612 | -0.8348355 | -0.8456677 | -0.8552042 | -0.8634898 | -0.8705677 | -0.8764801 | -0.8812678 | -0.8849706 | -0.8876273 | -0.8892760 | -0.8899536 | -0.8896966 | -0.8885408 | -0.8865214 | -0.8836732 | -0.8800305 | -0.8756274 | -0.8704975 | -0.8646744 | -0.8581915 | -0.8510820 | -0.8433792 | -0.8351162 | -0.8263265 | -0.8170433 | -0.8073002 | -0.7971309 | -0.7865694 | -0.7756497 | -0.7644063 | -0.7528740 | -0.7410879 | -0.7290834 | -0.7168963 | -0.7045628 | -0.6921196 | -0.6796035 |
| Nr1d1 | 2.3092053 | 2.2408024 | 2.1731343 | 2.1061427 | 2.0397718 | 1.9739678 | 1.9086797 | 1.8438586 | 1.7794577 | 1.7154328 | 1.6517416 | 1.5883440 | 1.5252022 | 1.4622803 | 1.3995448 | 1.3369640 | 1.2745085 | 1.2121508 | 1.1498655 | 1.0876292 | 1.0254207 | 0.9632207 | 0.9010118 | 0.8387788 | 0.7765290 | 0.7143707 | 0.6524368 | 0.5908536 | 0.5297403 | 0.4692096 | 0.4093671 | 0.3503124 | 0.2921385 | 0.2349323 | 0.1787748 | 0.1237415 | 0.0699023 | 0.0173224 | -0.0339383 | -0.0838239 | -0.1322831 | -0.1792682 | -0.2247351 | -0.2686429 | -0.3109537 | -0.3516319 | -0.3906443 | -0.4279594 | -0.4635472 | -0.4973791 | -0.5294269 | -0.5596634 | -0.5880675 | -0.6146823 | -0.6395842 | -0.6628461 | -0.6845366 | -0.7047210 | -0.7234609 | -0.7408148 | -0.7568385 | -0.7715848 | -0.7851040 | -0.7974441 | -0.8086510 | -0.8187686 | -0.8278388 | -0.8359019 | -0.8429966 | -0.8491602 | -0.8544286 | -0.8588367 | -0.8624181 | -0.8652054 | -0.8672306 | -0.8685245 | -0.8691175 | -0.8690393 | -0.8683189 | -0.8669851 | -0.8650661 | -0.8625898 | -0.8595839 | -0.8560759 | -0.8520931 | -0.8476627 | -0.8428120 | -0.8375679 | -0.8319580 | -0.8260094 | -0.8197496 | -0.8132062 | -0.8064072 | -0.7993805 | -0.7921546 | -0.7847579 | -0.7772194 | -0.7695683 | -0.7618342 | -0.7540471 |
| Klf9 | 2.3396649 | 2.2689335 | 2.1988336 | 2.1293311 | 2.0603931 | 1.9919880 | 1.9240851 | 1.8566550 | 1.7896695 | 1.7231015 | 1.6569250 | 1.5911152 | 1.5256486 | 1.4605025 | 1.3956556 | 1.3310877 | 1.2667796 | 1.2027135 | 1.1388725 | 1.0752409 | 1.0118042 | 0.9485490 | 0.8854630 | 0.8225352 | 0.7597726 | 0.6972650 | 0.6351234 | 0.5734536 | 0.5123565 | 0.4519277 | 0.3922583 | 0.3334340 | 0.2755362 | 0.2186412 | 0.1628212 | 0.1081437 | 0.0546721 | 0.0024661 | -0.0484189 | -0.0979307 | -0.1460206 | -0.1926431 | -0.2377554 | -0.2813175 | -0.3232916 | -0.3636422 | -0.4023354 | -0.4393390 | -0.4746221 | -0.5081546 | -0.5399072 | -0.5698508 | -0.5979629 | -0.6242823 | -0.6488806 | -0.6718261 | -0.6931839 | -0.7130159 | -0.7313808 | -0.7483349 | -0.7639317 | -0.7782223 | -0.7912557 | -0.8030786 | -0.8137360 | -0.8232708 | -0.8317245 | -0.8391370 | -0.8455466 | -0.8509906 | -0.8555050 | -0.8591245 | -0.8618831 | -0.8638138 | -0.8649487 | -0.8653193 | -0.8649566 | -0.8638908 | -0.8621516 | -0.8597687 | -0.8567709 | -0.8531871 | -0.8490459 | -0.8443758 | -0.8392050 | -0.8335618 | -0.8274747 | -0.8209718 | -0.8140815 | -0.8068326 | -0.7992536 | -0.7913736 | -0.7832216 | -0.7748272 | -0.7662199 | -0.7574299 | -0.7484875 | -0.7394233 | -0.7302685 | -0.7210545 |
| D130040H23Rik | 2.1775048 | 2.1049651 | 2.0337824 | 1.9639387 | 1.8954158 | 1.8281954 | 1.7622593 | 1.6975892 | 1.6341669 | 1.5719740 | 1.5109923 | 1.4512036 | 1.3925896 | 1.3351323 | 1.2788136 | 1.2236154 | 1.1695199 | 1.1165093 | 1.0645659 | 1.0136720 | 0.9638104 | 0.9149635 | 0.8671142 | 0.8202455 | 0.7743355 | 0.7293391 | 0.6852062 | 0.6418896 | 0.5993445 | 0.5575284 | 0.5164015 | 0.4759259 | 0.4360661 | 0.3967887 | 0.3580622 | 0.3198571 | 0.2821459 | 0.2449026 | 0.2081034 | 0.1717258 | 0.1357493 | 0.1001548 | 0.0649247 | 0.0300432 | -0.0045042 | -0.0387307 | -0.0726480 | -0.1062663 | -0.1395948 | -0.1726411 | -0.2054120 | -0.2379126 | -0.2701457 | -0.3020965 | -0.3337418 | -0.3650597 | -0.3960298 | -0.4266331 | -0.4568519 | -0.4866702 | -0.5160729 | -0.5450465 | -0.5735787 | -0.6016586 | -0.6292761 | -0.6564227 | -0.6830908 | -0.7092739 | -0.7349667 | -0.7601645 | -0.7848641 | -0.8090627 | -0.8327588 | -0.8559514 | -0.8786406 | -0.9008268 | -0.9225116 | -0.9436968 | -0.9643853 | -0.9845801 | -1.0042851 | -1.0235046 | -1.0422432 | -1.0605062 | -1.0782991 | -1.0956278 | -1.1124987 | -1.1289182 | -1.1448933 | -1.1604309 | -1.1755384 | -1.1902232 | -1.2044931 | -1.2183556 | -1.2318189 | -1.2448908 | -1.2575794 | -1.2698928 | -1.2818392 | -1.2934267 |
| D3Ertd254e | 2.6057166 | 2.4949461 | 2.3858907 | 2.2786514 | 2.1733226 | 2.0699916 | 1.9687397 | 1.8696416 | 1.7727668 | 1.6781788 | 1.5859362 | 1.4960929 | 1.4086979 | 1.3237964 | 1.2414296 | 1.1616353 | 1.0844481 | 1.0099001 | 0.9380205 | 0.8688367 | 0.8023743 | 0.7386576 | 0.6777097 | 0.6195530 | 0.5641859 | 0.5114928 | 0.4613285 | 0.4135543 | 0.3680374 | 0.3246505 | 0.2832716 | 0.2437830 | 0.2060718 | 0.1700290 | 0.1355494 | 0.1025312 | 0.0708761 | 0.0404887 | 0.0112762 | -0.0168514 | -0.0439816 | -0.0701999 | -0.0955894 | -0.1202316 | -0.1442059 | -0.1675900 | -0.1904600 | -0.2128905 | -0.2349546 | -0.2567240 | -0.2782688 | -0.2996582 | -0.3209558 | -0.3421842 | -0.3633430 | -0.3844315 | -0.4054489 | -0.4263945 | -0.4472676 | -0.4680676 | -0.4887939 | -0.5094457 | -0.5300226 | -0.5505237 | -0.5709486 | -0.5912968 | -0.6115675 | -0.6317603 | -0.6518746 | -0.6719099 | -0.6918657 | -0.7117415 | -0.7315369 | -0.7512513 | -0.7708843 | -0.7904354 | -0.8099043 | -0.8292905 | -0.8485935 | -0.8678132 | -0.8869489 | -0.9060005 | -0.9249674 | -0.9438495 | -0.9626463 | -0.9813576 | -0.9999830 | -1.0185223 | -1.0369752 | -1.0553413 | -1.0736205 | -1.0918125 | -1.1099171 | -1.1279340 | -1.1458630 | -1.1637040 | -1.1814567 | -1.1991210 | -1.2166966 | -1.2341835 |
| Heyl | 2.3614700 | 2.2781329 | 2.1963424 | 2.1160624 | 2.0372579 | 1.9598947 | 1.8839401 | 1.8093620 | 1.7361296 | 1.6642127 | 1.5935823 | 1.5242103 | 1.4560692 | 1.3891326 | 1.3233748 | 1.2587709 | 1.1952967 | 1.1329290 | 1.0716449 | 1.0114226 | 0.9522406 | 0.8940784 | 0.8369159 | 0.7807338 | 0.7255181 | 0.6712798 | 0.6180350 | 0.5657975 | 0.5145793 | 0.4643898 | 0.4152368 | 0.3671260 | 0.3200614 | 0.2740455 | 0.2290789 | 0.1851610 | 0.1422898 | 0.1004620 | 0.0596732 | 0.0199177 | -0.0188108 | -0.0565199 | -0.0932178 | -0.1289133 | -0.1636161 | -0.1973365 | -0.2300850 | -0.2618727 | -0.2927113 | -0.3226123 | -0.3515880 | -0.3796503 | -0.4068133 | -0.4331061 | -0.4585654 | -0.4832261 | -0.5071219 | -0.5302848 | -0.5527454 | -0.5745329 | -0.5956753 | -0.6161993 | -0.6361307 | -0.6554938 | -0.6743122 | -0.6926083 | -0.7104038 | -0.7277192 | -0.7445745 | -0.7609886 | -0.7769797 | -0.7925654 | -0.8077625 | -0.8225871 | -0.8370547 | -0.8511804 | -0.8649783 | -0.8784624 | -0.8916458 | -0.9045413 | -0.9171613 | -0.9295175 | -0.9416214 | -0.9534838 | -0.9651154 | -0.9765264 | -0.9877265 | -0.9987252 | -1.0095316 | -1.0201545 | -1.0306023 | -1.0408832 | -1.0510051 | -1.0609755 | -1.0708017 | -1.0804908 | -1.0900495 | -1.0994844 | -1.1088018 | -1.1180076 |
| Zbtb5 | 2.8112578 | 2.5911097 | 2.3792975 | 2.1761099 | 1.9817612 | 1.7963991 | 1.6201122 | 1.4529374 | 1.2948676 | 1.1458587 | 1.0058365 | 0.8747036 | 0.7523455 | 0.6386369 | 0.5334471 | 0.4366456 | 0.3481073 | 0.2677172 | 0.1953756 | 0.1310023 | 0.0745414 | 0.0259664 | -0.0147157 | -0.0474586 | -0.0722789 | -0.0896641 | -0.1001974 | -0.1044064 | -0.1027739 | -0.0957473 | -0.0837473 | -0.0671754 | -0.0464211 | -0.0218678 | 0.0061014 | 0.0370986 | 0.0707265 | 0.1065748 | 0.1442163 | 0.1832044 | 0.2230706 | 0.2633231 | 0.3034458 | 0.3428982 | 0.3811162 | 0.4175136 | 0.4514847 | 0.4824076 | 0.5096491 | 0.5325697 | 0.5505306 | 0.5629009 | 0.5691073 | 0.5690140 | 0.5627527 | 0.5504880 | 0.5324125 | 0.5087440 | 0.4797229 | 0.4456096 | 0.4066817 | 0.3632310 | 0.3155612 | 0.2639848 | 0.2088208 | 0.1503920 | 0.0890227 | 0.0250362 | -0.0412469 | -0.1095114 | -0.1794485 | -0.2507579 | -0.3231494 | -0.3963437 | -0.4700741 | -0.5440868 | -0.6181424 | -0.6920157 | -0.7654967 | -0.8383907 | -0.9105184 | -0.9817160 | -1.0518348 | -1.1207414 | -1.1883169 | -1.2544568 | -1.3190705 | -1.3820803 | -1.4434215 | -1.5030410 | -1.5608970 | -1.6169584 | -1.6712037 | -1.7236205 | -1.7742046 | -1.8229596 | -1.8698957 | -1.9150295 | -1.9583829 | -1.9999827 |
| Nkx6-2 | 2.7782970 | 2.5591456 | 2.3446750 | 2.1354347 | 1.9319273 | 1.7346102 | 1.5438975 | 1.3601628 | 1.1837418 | 1.0149359 | 0.8540150 | 0.7012214 | 0.5567736 | 0.4208704 | 0.2936945 | 0.1754172 | 0.0662028 | -0.0337873 | -0.1243897 | -0.2054346 | -0.2767404 | -0.3381094 | -0.3893221 | -0.4301319 | -0.4603999 | -0.4806325 | -0.4914969 | -0.4936176 | -0.4875838 | -0.4739568 | -0.4532761 | -0.4260659 | -0.3928400 | -0.3541073 | -0.3103759 | -0.2621577 | -0.2099717 | -0.1543474 | -0.0958276 | -0.0349711 | 0.0276460 | 0.0914283 | 0.1557602 | 0.2200055 | 0.2835073 | 0.3455887 | 0.4055536 | 0.4626886 | 0.5162651 | 0.5655420 | 0.6097690 | 0.6481908 | 0.6801003 | 0.7052850 | 0.7238281 | 0.7358329 | 0.7414186 | 0.7407189 | 0.7338815 | 0.7210667 | 0.7024464 | 0.6782030 | 0.6485288 | 0.6136244 | 0.5736982 | 0.5289649 | 0.4796452 | 0.4259643 | 0.3681512 | 0.3064379 | 0.2410586 | 0.1722483 | 0.1002428 | 0.0252774 | -0.0524136 | -0.1325977 | -0.2150450 | -0.2995284 | -0.3858246 | -0.4737147 | -0.5629841 | -0.6534237 | -0.7448299 | -0.8370051 | -0.9297581 | -1.0229044 | -1.1162662 | -1.2096731 | -1.3029617 | -1.3959764 | -1.4885690 | -1.5805988 | -1.6719329 | -1.7624461 | -1.8520207 | -1.9405465 | -2.0279209 | -2.1140484 | -2.1988409 | -2.2822170 |
| Rxrg | 1.2923771 | 1.1786689 | 1.0674405 | 0.9590672 | 0.8538940 | 0.7522376 | 0.6543879 | 0.5606107 | 0.4711493 | 0.3862277 | 0.3060526 | 0.2308168 | 0.1607016 | 0.0958801 | 0.0365205 | -0.0172108 | -0.0651459 | -0.1071116 | -0.1429259 | -0.1723941 | -0.1953048 | -0.2114254 | -0.2204977 | -0.2222332 | -0.2164219 | -0.2033769 | -0.1835507 | -0.1573721 | -0.1252529 | -0.0875954 | -0.0447982 | 0.0027382 | 0.0546060 | 0.1103850 | 0.1696392 | 0.2319118 | 0.2967227 | 0.3635654 | 0.4319047 | 0.5011750 | 0.5707793 | 0.6400889 | 0.7084436 | 0.7751530 | 0.8394985 | 0.9007356 | 0.9580980 | 1.0108016 | 1.0580504 | 1.0990421 | 1.1329756 | 1.1590586 | 1.1765678 | 1.1853195 | 1.1854603 | 1.1771767 | 1.1606890 | 1.1362489 | 1.1041364 | 1.0646575 | 1.0181410 | 0.9649362 | 0.9054096 | 0.8399426 | 0.7689287 | 0.6927707 | 0.6118781 | 0.5266646 | 0.4375459 | 0.3449369 | 0.2492496 | 0.1508912 | 0.0502617 | -0.0522477 | -0.1562565 | -0.2613965 | -0.3673131 | -0.4736668 | -0.5801341 | -0.6864087 | -0.7922019 | -0.8972435 | -1.0012824 | -1.1040864 | -1.2054426 | -1.3051576 | -1.4030570 | -1.4989852 | -1.5928050 | -1.6843972 | -1.7736598 | -1.8605075 | -1.9448708 | -2.0266950 | -2.1059398 | -2.1825779 | -2.2565945 | -2.3279858 | -2.3967587 | -2.4629293 |
| Pax6 | 1.3795954 | 1.2756736 | 1.1740674 | 1.0751188 | 0.9791412 | 0.8864207 | 0.7972177 | 0.7117689 | 0.6302893 | 0.5529743 | 0.4800028 | 0.4115390 | 0.3477358 | 0.2887376 | 0.2346831 | 0.1857087 | 0.1419517 | 0.1035536 | 0.0706639 | 0.0434435 | 0.0220686 | 0.0067352 | -0.0023373 | -0.0049007 | -0.0007783 | 0.0097297 | 0.0261963 | 0.0482168 | 0.0754016 | 0.1073690 | 0.1437399 | 0.1841315 | 0.2281529 | 0.2754002 | 0.3254526 | 0.3778690 | 0.4321851 | 0.4879109 | 0.5445291 | 0.6014942 | 0.6582321 | 0.7141401 | 0.7685888 | 0.8209232 | 0.8704659 | 0.9165207 | 0.9583767 | 0.9953135 | 1.0266075 | 1.0515386 | 1.0693977 | 1.0794952 | 1.0812177 | 1.0744626 | 1.0594395 | 1.0363998 | 1.0056296 | 0.9674473 | 0.9221999 | 0.8702601 | 0.8120229 | 0.7479025 | 0.6783290 | 0.6037449 | 0.5246025 | 0.4413601 | 0.3544794 | 0.2644222 | 0.1716473 | 0.0766080 | -0.0202509 | -0.1184956 | -0.2177057 | -0.3174766 | -0.4174213 | -0.5171723 | -0.6163833 | -0.7147306 | -0.8119138 | -0.9076570 | -1.0017092 | -1.0938446 | -1.1838627 | -1.2715879 | -1.3568694 | -1.4395804 | -1.5196173 | -1.5968984 | -1.6713633 | -1.7429714 | -1.8117004 | -1.8775451 | -1.9405157 | -2.0006367 | -2.0579450 | -2.1124886 | -2.1643254 | -2.2135214 | -2.2601495 | -2.3042887 |
| Rit1 | 1.5555199 | 1.4676359 | 1.3808177 | 1.2953330 | 1.2114395 | 1.1293857 | 1.0494106 | 0.9717449 | 0.8966110 | 0.8242239 | 0.7547917 | 0.6885165 | 0.6255953 | 0.5662205 | 0.5105812 | 0.4588638 | 0.4112537 | 0.3679354 | 0.3290948 | 0.2949193 | 0.2656001 | 0.2413327 | 0.2223188 | 0.2087679 | 0.2008133 | 0.1981837 | 0.2004919 | 0.2073600 | 0.2184170 | 0.2332967 | 0.2516363 | 0.2730737 | 0.2972471 | 0.3237927 | 0.3523441 | 0.3825310 | 0.4139786 | 0.4463066 | 0.4791291 | 0.5120538 | 0.5446827 | 0.5766112 | 0.6074290 | 0.6367204 | 0.6640650 | 0.6890382 | 0.7112128 | 0.7301598 | 0.7454503 | 0.7566564 | 0.7633538 | 0.7651236 | 0.7615856 | 0.7526799 | 0.7385349 | 0.7192900 | 0.6950926 | 0.6660976 | 0.6324665 | 0.5943670 | 0.5519718 | 0.5054584 | 0.4550082 | 0.4008059 | 0.3430388 | 0.2818964 | 0.2175693 | 0.1502491 | 0.0801277 | 0.0073966 | -0.0677535 | -0.1451331 | -0.2245546 | -0.3058326 | -0.3887843 | -0.4732302 | -0.5589939 | -0.6459029 | -0.7337890 | -0.8224881 | -0.9118408 | -1.0016927 | -1.0918944 | -1.1823018 | -1.2727762 | -1.3631844 | -1.4533990 | -1.5432981 | -1.6327658 | -1.7216918 | -1.8099718 | -1.8975071 | -1.9842050 | -2.0699782 | -2.1547452 | -2.2384300 | -2.3209621 | -2.4022761 | -2.4823119 | -2.5610144 |
| Tsc22d3 | 1.7908200 | 1.6989762 | 1.6081299 | 1.5185296 | 1.4304158 | 1.3440207 | 1.2595689 | 1.1772774 | 1.0973562 | 1.0200087 | 0.9454321 | 0.8738181 | 0.8053535 | 0.7402205 | 0.6785978 | 0.6206613 | 0.5665847 | 0.5165403 | 0.4707002 | 0.4292369 | 0.3923245 | 0.3601395 | 0.3328622 | 0.3106774 | 0.2936993 | 0.2816742 | 0.2742435 | 0.2710569 | 0.2717709 | 0.2760471 | 0.2835512 | 0.2939512 | 0.3069168 | 0.3221178 | 0.3392238 | 0.3579031 | 0.3778221 | 0.3986449 | 0.4200327 | 0.4416439 | 0.4631334 | 0.4841533 | 0.5043524 | 0.5233767 | 0.5408700 | 0.5564739 | 0.5698288 | 0.5805748 | 0.5883522 | 0.5928027 | 0.5935707 | 0.5903045 | 0.5826841 | 0.5706606 | 0.5543423 | 0.5338450 | 0.5092892 | 0.4807997 | 0.4485053 | 0.4125386 | 0.3730350 | 0.3301328 | 0.2839727 | 0.2346972 | 0.1824504 | 0.1273776 | 0.0696250 | 0.0093391 | -0.0533333 | -0.1182457 | -0.1852519 | -0.2542067 | -0.3249659 | -0.3973868 | -0.4713282 | -0.5466508 | -0.6232175 | -0.7008935 | -0.7795464 | -0.8590469 | -0.9392682 | -1.0200870 | -1.1013829 | -1.1830391 | -1.2649421 | -1.3469821 | -1.4290530 | -1.5110525 | -1.5928819 | -1.6744466 | -1.7556559 | -1.8364228 | -1.9166645 | -1.9963020 | -2.0752601 | -2.1534677 | -2.2308575 | -2.3073657 | -2.3829326 | -2.4575021 |
| Arntl | 1.7438245 | 1.6424515 | 1.5430140 | 1.4457834 | 1.3510119 | 1.2589339 | 1.1697666 | 1.0837115 | 1.0009560 | 0.9216740 | 0.8460282 | 0.7741711 | 0.7062469 | 0.6423929 | 0.5827413 | 0.5274210 | 0.4765593 | 0.4302838 | 0.3887243 | 0.3520148 | 0.3202955 | 0.2937149 | 0.2724324 | 0.2566201 | 0.2463807 | 0.2414194 | 0.2413341 | 0.2457394 | 0.2542624 | 0.2665393 | 0.2822120 | 0.3009252 | 0.3223238 | 0.3460508 | 0.3717447 | 0.3990385 | 0.4275575 | 0.4569189 | 0.4867304 | 0.5165900 | 0.5460855 | 0.5747953 | 0.6022880 | 0.6281241 | 0.6518570 | 0.6730342 | 0.6912001 | 0.7058978 | 0.7166722 | 0.7230730 | 0.7246584 | 0.7209990 | 0.7117141 | 0.6967676 | 0.6763274 | 0.6505799 | 0.6197263 | 0.5839805 | 0.5435681 | 0.4987245 | 0.4496934 | 0.3967249 | 0.3400747 | 0.2800019 | 0.2167681 | 0.1506357 | 0.0818667 | 0.0107216 | -0.0625421 | -0.1376707 | -0.2144153 | -0.2925330 | -0.3717875 | -0.4519499 | -0.5327994 | -0.6141241 | -0.6957209 | -0.7773967 | -0.8589681 | -0.9402620 | -1.0211157 | -1.1013770 | -1.1809043 | -1.2595662 | -1.3372422 | -1.4138219 | -1.4892049 | -1.5633009 | -1.6360290 | -1.7073178 | -1.7771046 | -1.8453356 | -1.9119650 | -1.9769549 | -2.0402747 | -2.1019007 | -2.1618160 | -2.2200094 | -2.2764757 | -2.3312146 |
| Nfib | 0.1628424 | 0.1667088 | 0.1706506 | 0.1747423 | 0.1790588 | 0.1836747 | 0.1886648 | 0.1941043 | 0.2000680 | 0.2066312 | 0.2138693 | 0.2218578 | 0.2306724 | 0.2403891 | 0.2510843 | 0.2628344 | 0.2757163 | 0.2898074 | 0.3051855 | 0.3219287 | 0.3401158 | 0.3598261 | 0.3811396 | 0.4041370 | 0.4288599 | 0.4551560 | 0.4828126 | 0.5116163 | 0.5413525 | 0.5718054 | 0.6027580 | 0.6339919 | 0.6652875 | 0.6964236 | 0.7271778 | 0.7573265 | 0.7866446 | 0.8149061 | 0.8418839 | 0.8673499 | 0.8910754 | 0.9128309 | 0.9323868 | 0.9495131 | 0.9639801 | 0.9755584 | 0.9840191 | 0.9891344 | 0.9906778 | 0.9884244 | 0.9821513 | 0.9716380 | 0.9566861 | 0.9372898 | 0.9135545 | 0.8855896 | 0.8535064 | 0.8174183 | 0.7774405 | 0.7336900 | 0.6862852 | 0.6353459 | 0.5809931 | 0.5233490 | 0.4625367 | 0.3986801 | 0.3319039 | 0.2623331 | 0.1900933 | 0.1153104 | 0.0381103 | -0.0413808 | -0.1230372 | -0.2067330 | -0.2923430 | -0.3797424 | -0.4688068 | -0.5594127 | -0.6514376 | -0.7447598 | -0.8392586 | -0.9348146 | -1.0313100 | -1.1286280 | -1.2266538 | -1.3252738 | -1.4243765 | -1.5238523 | -1.6235935 | -1.7234943 | -1.8234513 | -1.9233632 | -2.0231313 | -2.1226590 | -2.2218523 | -2.3206197 | -2.4188724 | -2.5165242 | -2.6134916 | -2.7096938 |
| Nfe2l2 | 1.0277721 | 0.9660517 | 0.9053617 | 0.8459415 | 0.7880180 | 0.7318061 | 0.6775098 | 0.6253228 | 0.5754295 | 0.5280061 | 0.4832216 | 0.4412391 | 0.4022174 | 0.3663117 | 0.3336757 | 0.3044628 | 0.2788278 | 0.2569288 | 0.2389285 | 0.2249967 | 0.2153121 | 0.2100643 | 0.2094562 | 0.2137067 | 0.2229690 | 0.2370026 | 0.2554544 | 0.2779792 | 0.3042359 | 0.3338839 | 0.3665794 | 0.4019727 | 0.4397053 | 0.4794079 | 0.5206978 | 0.5631778 | 0.6064348 | 0.6500388 | 0.6935424 | 0.7364812 | 0.7783738 | 0.8187231 | 0.8570173 | 0.8927323 | 0.9253340 | 0.9542814 | 0.9790299 | 0.9990356 | 1.0137602 | 1.0226756 | 1.0252697 | 1.0210525 | 1.0096003 | 0.9908999 | 0.9651855 | 0.9327213 | 0.8937963 | 0.8487216 | 0.7978274 | 0.7414602 | 0.6799801 | 0.6137582 | 0.5431733 | 0.4686097 | 0.3904548 | 0.3090960 | 0.2249188 | 0.1383045 | 0.0496279 | -0.0407446 | -0.1324566 | -0.2251635 | -0.3185343 | -0.4122522 | -0.5060164 | -0.5995425 | -0.6925637 | -0.7848311 | -0.8761143 | -0.9662014 | -1.0548993 | -1.1420335 | -1.2274480 | -1.3110050 | -1.3925841 | -1.4720821 | -1.5494124 | -1.6245038 | -1.6973001 | -1.7677594 | -1.8358524 | -1.9015626 | -1.9648845 | -2.0258230 | -2.0843924 | -2.1406157 | -2.1945233 | -2.2461523 | -2.2955459 | -2.3427523 |
| Meis2 | 0.7917188 | 0.7563692 | 0.7214179 | 0.6870354 | 0.6533879 | 0.6206373 | 0.5889418 | 0.5584557 | 0.5293300 | 0.5017128 | 0.4757496 | 0.4515838 | 0.4293572 | 0.4092107 | 0.3912848 | 0.3757204 | 0.3626595 | 0.3522456 | 0.3446253 | 0.3399485 | 0.3383696 | 0.3400485 | 0.3451517 | 0.3538533 | 0.3662692 | 0.3821953 | 0.4013312 | 0.4233778 | 0.4480355 | 0.4750024 | 0.5039726 | 0.5346349 | 0.5666717 | 0.5997579 | 0.6335606 | 0.6677381 | 0.7019401 | 0.7358071 | 0.7689714 | 0.8010566 | 0.8316791 | 0.8604485 | 0.8869690 | 0.9108404 | 0.9316604 | 0.9490258 | 0.9625351 | 0.9717903 | 0.9764002 | 0.9759826 | 0.9701676 | 0.9586008 | 0.9409767 | 0.9173076 | 0.8877943 | 0.8526555 | 0.8121240 | 0.7664455 | 0.7158772 | 0.6606863 | 0.6011484 | 0.5375466 | 0.4701697 | 0.3993108 | 0.3252662 | 0.2483339 | 0.1688123 | 0.0869986 | 0.0031882 | -0.0823273 | -0.1692610 | -0.2573315 | -0.3462648 | -0.4357947 | -0.5256639 | -0.6156250 | -0.7054416 | -0.7948884 | -0.8837524 | -0.9718330 | -1.0589431 | -1.1449086 | -1.2295693 | -1.3127789 | -1.3944047 | -1.4743280 | -1.5524437 | -1.6286602 | -1.7028988 | -1.7750938 | -1.8451912 | -1.9131494 | -1.9789373 | -2.0425346 | -2.1039309 | -2.1631248 | -2.2201235 | -2.2749418 | -2.3276017 | -2.3781316 |
| Id2 | 0.8958120 | 0.8541181 | 0.8127755 | 0.7719685 | 0.7318786 | 0.6926838 | 0.6545595 | 0.6176778 | 0.5822082 | 0.5483175 | 0.5161700 | 0.4859279 | 0.4577516 | 0.4318000 | 0.4082311 | 0.3872023 | 0.3688711 | 0.3533958 | 0.3409358 | 0.3316526 | 0.3257104 | 0.3232770 | 0.3245244 | 0.3296297 | 0.3387070 | 0.3515389 | 0.3678079 | 0.3871987 | 0.4093962 | 0.4340844 | 0.4609454 | 0.4896584 | 0.5198988 | 0.5513381 | 0.5836430 | 0.6164755 | 0.6494923 | 0.6823455 | 0.7146823 | 0.7461454 | 0.7763734 | 0.8050014 | 0.8316614 | 0.8559831 | 0.8775949 | 0.8961243 | 0.9111993 | 0.9224491 | 0.9295055 | 0.9320042 | 0.9295858 | 0.9218979 | 0.9086246 | 0.8897426 | 0.8653995 | 0.8357529 | 0.8009683 | 0.7612187 | 0.7166842 | 0.6675523 | 0.6140174 | 0.5562808 | 0.4945507 | 0.4290416 | 0.3599749 | 0.2875782 | 0.2120852 | 0.1337356 | 0.0527748 | -0.0305466 | -0.1159729 | -0.2032445 | -0.2920977 | -0.3822659 | -0.4734806 | -0.5654717 | -0.6579694 | -0.7507047 | -0.8434112 | -0.9358262 | -1.0276924 | -1.1187592 | -1.2087847 | -1.2975368 | -1.3847954 | -1.4703533 | -1.5540181 | -1.6356134 | -1.7149797 | -1.7919759 | -1.8664795 | -1.9383871 | -2.0076153 | -2.0740996 | -2.1377952 | -2.1986756 | -2.2567322 | -2.3119733 | -2.3644227 | -2.4141189 |
write.table(heatmap_matrix_q_value_5_10_minus_5, file = file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
significant_genes_q_value_0.01 <- filter(diff_test_res_all_genes, qval < 0.01) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))
## Number of significant genes: 7357
significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))
## Number of significant transcription factors: 384
plot_genes_heatmap_output_q_value_0.01 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)
## <simpleError in checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon): NAs found in the working weights variable 'wz'>
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_0.01[[2]], file.path("figures", "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6", "diff_test_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=40)
## pdf
## 2
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
ph_res_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[2]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])
transcription_factors_table_q_value_0.01 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6-significant_transcription_factors_diff_test_analysis_qval_0.01.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
heatmap_matrix_q_value_0.01 <- as.data.frame(heatmap_matrix_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_q_value_0.01 <- heatmap_matrix_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
| gene | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Pou3f2 | -0.1297400 | -0.0154223 | 0.0996139 | 0.2148745 | 0.3298456 | 0.4439934 | 0.5567651 | 0.6675897 | 0.7758786 | 0.8810272 | 0.9824160 | 1.0794130 | 1.1713751 | 1.2576504 | 1.3375813 | 1.4105066 | 1.4757646 | 1.5326969 | 1.5806511 | 1.6189851 | 1.6470708 | 1.6642984 | 1.6700805 | 1.6638570 | 1.6452683 | 1.6148154 | 1.5732786 | 1.5214585 | 1.4601698 | 1.3902364 | 1.3124859 | 1.2277455 | 1.1368372 | 1.0405744 | 0.9397585 | 0.8351754 | 0.7275936 | 0.6177615 | 0.5064061 | 0.3942310 | 0.2819159 | 0.1701162 | 0.0594620 | -0.0494410 | -0.1560111 | -0.2596901 | -0.3599419 | -0.4562510 | -0.5481207 | -0.6350710 | -0.7166363 | -0.7923628 | -0.8618465 | -0.9250958 | -0.9823434 | -1.0338113 | -1.0797086 | -1.1202328 | -1.1555702 | -1.1858968 | -1.2113791 | -1.2321747 | -1.2484330 | -1.2602957 | -1.2678978 | -1.2713675 | -1.2708276 | -1.2663953 | -1.2581831 | -1.2462990 | -1.2308473 | -1.2119290 | -1.1896419 | -1.1640812 | -1.1353400 | -1.1035098 | -1.0686804 | -1.0309405 | -0.9903784 | -0.9470817 | -0.9011380 | -0.8526352 | -0.8016617 | -0.7483065 | -0.6926599 | -0.6348136 | -0.5748606 | -0.5128960 | -0.4490167 | -0.3833220 | -0.3159136 | -0.2468960 | -0.1763762 | -0.1044645 | -0.0312741 | 0.0430783 | 0.1184729 | 0.1947863 | 0.2718913 | 0.3496575 |
| Sp6 | 0.5839400 | 0.5938060 | 0.6039331 | 0.6145201 | 0.6257716 | 0.6378991 | 0.6511220 | 0.6656688 | 0.6817789 | 0.6997049 | 0.7197148 | 0.7420951 | 0.7671546 | 0.7952279 | 0.8266807 | 0.8619151 | 0.9013762 | 0.9455596 | 0.9950205 | 1.0503840 | 1.1123574 | 1.1817451 | 1.2594654 | 1.3465714 | 1.4435754 | 1.5474623 | 1.6534536 | 1.7558789 | 1.8481991 | 1.9231748 | 1.9732066 | 1.9908545 | 1.9695176 | 1.9042177 | 1.7923907 | 1.6345551 | 1.4347129 | 1.2003503 | 0.9419577 | 0.6720730 | 0.4039581 | 0.1501115 | -0.0791159 | -0.2765450 | -0.4386476 | -0.5654235 | -0.6597598 | -0.7264654 | -0.7712238 | -0.7996785 | -0.8167904 | -0.8265083 | -0.8317101 | -0.8343260 | -0.8355620 | -0.8361119 | -0.8363426 | -0.8364341 | -0.8364685 | -0.8364807 | -0.8364849 | -0.8364862 | -0.8364866 | -0.8364867 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 | -0.8364868 |
| Irx3 | 2.0868433 | 2.0293431 | 1.9719996 | 1.9147184 | 1.8574065 | 1.7999728 | 1.7423279 | 1.6843840 | 1.6260552 | 1.5672573 | 1.5079080 | 1.4479267 | 1.3872349 | 1.3257560 | 1.2634155 | 1.2001409 | 1.1358619 | 1.0705106 | 1.0040213 | 0.9363307 | 0.8673781 | 0.7971054 | 0.7254570 | 0.6523805 | 0.5778709 | 0.5021436 | 0.4254760 | 0.3481387 | 0.2703957 | 0.1925038 | 0.1147131 | 0.0372661 | -0.0396016 | -0.1156614 | -0.1906918 | -0.2644782 | -0.3368125 | -0.4074930 | -0.4763238 | -0.5431149 | -0.6076815 | -0.6698437 | -0.7294258 | -0.7862560 | -0.8401657 | -0.8909890 | -0.9385620 | -0.9827221 | -1.0233073 | -1.0601556 | -1.0931039 | -1.1219875 | -1.1466565 | -1.1671324 | -1.1835312 | -1.1959634 | -1.2045335 | -1.2093403 | -1.2104776 | -1.2080341 | -1.2020942 | -1.1927381 | -1.1800423 | -1.1640799 | -1.1449206 | -1.1226317 | -1.0972777 | -1.0689209 | -1.0376217 | -1.0034387 | -0.9664293 | -0.9266495 | -0.8841544 | -0.8389985 | -0.7912356 | -0.7409196 | -0.6881040 | -0.6328429 | -0.5751904 | -0.5152015 | -0.4529319 | -0.3884382 | -0.3217784 | -0.2530117 | -0.1821989 | -0.1094025 | -0.0346870 | 0.0418813 | 0.1202337 | 0.2002991 | 0.2820041 | 0.3652726 | 0.4500256 | 0.5361814 | 0.6236553 | 0.7123595 | 0.8022030 | 0.8930914 | 0.9849271 | 1.0776091 |
| Rora | 2.2655226 | 2.1976372 | 2.1300251 | 2.0626244 | 1.9953746 | 1.9282164 | 1.8610915 | 1.7939432 | 1.7267158 | 1.6593550 | 1.5918075 | 1.5240216 | 1.4559467 | 1.3875337 | 1.3187346 | 1.2495029 | 1.1797935 | 1.1095627 | 1.0387683 | 0.9673693 | 0.8953266 | 0.8226024 | 0.7491605 | 0.6749663 | 0.6000216 | 0.5244968 | 0.4486094 | 0.3725718 | 0.2965908 | 0.2208676 | 0.1455983 | 0.0709731 | -0.0028230 | -0.0756103 | -0.1472145 | -0.2174661 | -0.2862006 | -0.3532582 | -0.4184832 | -0.4817242 | -0.5428335 | -0.6016669 | -0.6580833 | -0.7119441 | -0.7631132 | -0.8114562 | -0.8568401 | -0.8991328 | -0.9382024 | -0.9739171 | -1.0061441 | -1.0347492 | -1.0596114 | -1.0807534 | -1.0982781 | -1.1122840 | -1.1228651 | -1.1301108 | -1.1341066 | -1.1349342 | -1.1326717 | -1.1273941 | -1.1191733 | -1.1080786 | -1.0941767 | -1.0775324 | -1.0582082 | -1.0362650 | -1.0117619 | -0.9847570 | -0.9553071 | -0.9234679 | -0.8892945 | -0.8528415 | -0.8141629 | -0.7733126 | -0.7303444 | -0.6853122 | -0.6382702 | -0.5892729 | -0.5383755 | -0.4856339 | -0.4311047 | -0.3748457 | -0.3169156 | -0.2573744 | -0.1962836 | -0.1337059 | -0.0697059 | -0.0043496 | 0.0622950 | 0.1301582 | 0.1991683 | 0.2692515 | 0.3403318 | 0.4123311 | 0.4851692 | 0.5587634 | 0.6330286 | 0.7078775 |
| Zfp112 | 0.8745833 | 0.9250182 | 0.9757078 | 1.0263301 | 1.0765490 | 1.1260144 | 1.1743630 | 1.2212187 | 1.2661940 | 1.3088907 | 1.3489019 | 1.3858140 | 1.4192085 | 1.4486648 | 1.4737632 | 1.4940875 | 1.5092291 | 1.5187901 | 1.5223876 | 1.5196576 | 1.5102593 | 1.4938796 | 1.4702374 | 1.4390878 | 1.4003333 | 1.3544330 | 1.3020230 | 1.2437480 | 1.1802542 | 1.1121830 | 1.0401661 | 0.9648198 | 0.8867414 | 0.8065054 | 0.7246610 | 0.6417294 | 0.5582025 | 0.4745417 | 0.3911775 | 0.3085092 | 0.2269054 | 0.1467048 | 0.0682171 | -0.0082758 | -0.0825179 | -0.1542774 | -0.2233452 | -0.2895322 | -0.3526675 | -0.4125960 | -0.4691763 | -0.5222778 | -0.5717985 | -0.6178313 | -0.6605687 | -0.7001902 | -0.7368623 | -0.7707398 | -0.8019663 | -0.8306755 | -0.8569918 | -0.8810314 | -0.9029026 | -0.9227067 | -0.9405385 | -0.9564868 | -0.9706352 | -0.9830622 | -0.9938416 | -1.0030436 | -1.0107341 | -1.0169761 | -1.0218292 | -1.0253505 | -1.0275945 | -1.0286135 | -1.0284581 | -1.0271769 | -1.0248172 | -1.0214250 | -1.0170453 | -1.0117222 | -1.0054990 | -0.9984188 | -0.9905240 | -0.9818570 | -0.9724600 | -0.9623755 | -0.9516460 | -0.9403144 | -0.9284241 | -0.9160191 | -0.9031437 | -0.8898435 | -0.8761643 | -0.8621534 | -0.8478586 | -0.8333290 | -0.8186146 | -0.8037666 |
| Atf7 | 1.2090613 | 1.2293352 | 1.2494540 | 1.2692130 | 1.2884055 | 1.3068230 | 1.3242556 | 1.3404920 | 1.3553198 | 1.3685259 | 1.3798967 | 1.3892185 | 1.3962784 | 1.4008643 | 1.4027656 | 1.4017738 | 1.3976836 | 1.3902927 | 1.3794035 | 1.3648232 | 1.3463650 | 1.3238488 | 1.2971022 | 1.2659612 | 1.2303341 | 1.1904441 | 1.1466110 | 1.0991549 | 1.0483952 | 0.9946492 | 0.9382312 | 0.8794516 | 0.8186155 | 0.7560227 | 0.6919664 | 0.6267329 | 0.5606011 | 0.4938422 | 0.4267193 | 0.3594870 | 0.2923919 | 0.2256720 | 0.1595568 | 0.0942679 | 0.0300185 | -0.0329858 | -0.0945468 | -0.1544736 | -0.2125816 | -0.2686928 | -0.3226344 | -0.3742390 | -0.4233584 | -0.4699989 | -0.5142512 | -0.5562032 | -0.5959394 | -0.6335412 | -0.6690867 | -0.7026510 | -0.7343066 | -0.7641234 | -0.7921689 | -0.8185084 | -0.8432048 | -0.8663194 | -0.8879114 | -0.9080383 | -0.9267560 | -0.9441189 | -0.9601802 | -0.9749913 | -0.9886031 | -1.0010647 | -1.0124247 | -1.0227305 | -1.0320288 | -1.0403653 | -1.0477853 | -1.0543332 | -1.0600528 | -1.0649878 | -1.0691808 | -1.0726746 | -1.0755112 | -1.0777326 | -1.0793803 | -1.0804958 | -1.0811202 | -1.0812946 | -1.0810600 | -1.0804572 | -1.0795270 | -1.0783103 | -1.0768476 | -1.0751799 | -1.0733478 | -1.0713923 | -1.0693542 | -1.0672743 |
| Zfp521 | 1.3555900 | 1.3713142 | 1.3868412 | 1.4019436 | 1.4163922 | 1.4299564 | 1.4424048 | 1.4535045 | 1.4630225 | 1.4707253 | 1.4763798 | 1.4797536 | 1.4806155 | 1.4787364 | 1.4738899 | 1.4658529 | 1.4544064 | 1.4393365 | 1.4204353 | 1.3975018 | 1.3703428 | 1.3387739 | 1.3026209 | 1.2617203 | 1.2159935 | 1.1657267 | 1.1113163 | 1.0531569 | 0.9916403 | 0.9271533 | 0.8600767 | 0.7907841 | 0.7196406 | 0.6470022 | 0.5732148 | 0.4986137 | 0.4235233 | 0.3482564 | 0.2731145 | 0.1983871 | 0.1243525 | 0.0512774 | -0.0205828 | -0.0909831 | -0.1596892 | -0.2264764 | -0.2911292 | -0.3534404 | -0.4132106 | -0.4702471 | -0.5243634 | -0.5753776 | -0.6231301 | -0.6676447 | -0.7090449 | -0.7474490 | -0.7829697 | -0.8157141 | -0.8457845 | -0.8732780 | -0.8982878 | -0.9209027 | -0.9412077 | -0.9592845 | -0.9752111 | -0.9890630 | -1.0009125 | -1.0108296 | -1.0188818 | -1.0251345 | -1.0296512 | -1.0324934 | -1.0337214 | -1.0333936 | -1.0315676 | -1.0282995 | -1.0236447 | -1.0176575 | -1.0103917 | -1.0019004 | -0.9922364 | -0.9814520 | -0.9695992 | -0.9567301 | -0.9428966 | -0.9281507 | -0.9125446 | -0.8961306 | -0.8789614 | -0.8610901 | -0.8425703 | -0.8234560 | -0.8038017 | -0.7836628 | -0.7630951 | -0.7421554 | -0.7209009 | -0.6993899 | -0.6776814 | -0.6558352 |
| Zfp768 | 1.7015702 | 1.6867105 | 1.6717388 | 1.6565224 | 1.6409293 | 1.6248286 | 1.6080900 | 1.5905845 | 1.5721838 | 1.5527612 | 1.5321908 | 1.5103486 | 1.4871119 | 1.4623599 | 1.4359737 | 1.4078365 | 1.3778339 | 1.3458540 | 1.3117879 | 1.2755296 | 1.2369764 | 1.1960293 | 1.1525933 | 1.1065771 | 1.0579378 | 1.0068476 | 0.9535423 | 0.8982551 | 0.8412159 | 0.7826511 | 0.7227832 | 0.6618302 | 0.6000059 | 0.5375188 | 0.4745729 | 0.4113667 | 0.3480938 | 0.2849424 | 0.2220953 | 0.1597304 | 0.0980200 | 0.0371318 | -0.0227719 | -0.0815331 | -0.1389987 | -0.1950197 | -0.2494513 | -0.3021523 | -0.3529851 | -0.4018151 | -0.4485105 | -0.4929418 | -0.5349940 | -0.5746766 | -0.6120682 | -0.6472452 | -0.6802815 | -0.7112481 | -0.7402140 | -0.7672455 | -0.7924071 | -0.8157611 | -0.8373679 | -0.8572863 | -0.8755734 | -0.8922848 | -0.9074745 | -0.9211956 | -0.9334994 | -0.9444366 | -0.9540566 | -0.9624078 | -0.9695378 | -0.9754936 | -0.9803210 | -0.9840657 | -0.9867724 | -0.9884854 | -0.9892487 | -0.9891056 | -0.9880993 | -0.9862725 | -0.9836680 | -0.9803279 | -0.9762947 | -0.9716103 | -0.9663167 | -0.9604561 | -0.9540704 | -0.9472016 | -0.9398919 | -0.9321834 | -0.9241184 | -0.9157394 | -0.9070889 | -0.8982097 | -0.8891448 | -0.8799372 | -0.8706305 | -0.8612680 |
| Epas1 | 1.5483476 | 1.5479212 | 1.5472907 | 1.5462522 | 1.5446019 | 1.5421370 | 1.5386553 | 1.5339564 | 1.5278421 | 1.5201168 | 1.5105889 | 1.4990712 | 1.4853825 | 1.4693482 | 1.4508017 | 1.4295857 | 1.4055536 | 1.3785707 | 1.3485158 | 1.3152823 | 1.2787803 | 1.2389371 | 1.1956993 | 1.1490337 | 1.0989829 | 1.0458695 | 0.9900946 | 0.9320508 | 0.8721196 | 0.8106691 | 0.7480520 | 0.6846040 | 0.6206421 | 0.5564639 | 0.4923469 | 0.4285480 | 0.3653033 | 0.3028282 | 0.2413179 | 0.1809474 | 0.1218727 | 0.0642314 | 0.0081434 | -0.0462876 | -0.0989737 | -0.1498408 | -0.1988283 | -0.2458874 | -0.2909797 | -0.3340765 | -0.3751576 | -0.4142094 | -0.4512326 | -0.4863069 | -0.5195503 | -0.5510732 | -0.5809785 | -0.6093625 | -0.6363150 | -0.6619199 | -0.6862557 | -0.7093960 | -0.7314096 | -0.7523612 | -0.7723114 | -0.7913171 | -0.8094318 | -0.8267059 | -0.8431868 | -0.8589193 | -0.8739455 | -0.8883053 | -0.9020363 | -0.9151743 | -0.9277531 | -0.9398047 | -0.9513595 | -0.9624464 | -0.9730931 | -0.9833258 | -0.9931694 | -1.0026479 | -1.0117841 | -1.0205999 | -1.0291163 | -1.0373533 | -1.0453303 | -1.0530657 | -1.0605774 | -1.0678826 | -1.0749979 | -1.0819392 | -1.0887219 | -1.0953610 | -1.1018707 | -1.1082651 | -1.1145575 | -1.1207610 | -1.1268882 | -1.1329512 |
| Nr3c2 | 1.3601806 | 1.3894666 | 1.4186106 | 1.4472205 | 1.4748919 | 1.5012095 | 1.5257484 | 1.5480754 | 1.5677513 | 1.5843341 | 1.5973815 | 1.6064551 | 1.6111242 | 1.6109706 | 1.6055932 | 1.5946137 | 1.5776815 | 1.5544802 | 1.5247325 | 1.4882066 | 1.4447215 | 1.3941521 | 1.3364343 | 1.2715693 | 1.1997494 | 1.1218119 | 1.0387691 | 0.9516035 | 0.8612568 | 0.7686201 | 0.6745267 | 0.5797467 | 0.4849838 | 0.3908731 | 0.2979813 | 0.2068076 | 0.1177857 | 0.0312873 | -0.0523748 | -0.1329418 | -0.2102047 | -0.2839990 | -0.3542001 | -0.4207180 | -0.4834924 | -0.5424883 | -0.5976907 | -0.6491009 | -0.6967317 | -0.7406038 | -0.7807420 | -0.8171712 | -0.8499298 | -0.8792065 | -0.9052557 | -0.9283040 | -0.9485526 | -0.9661799 | -0.9813441 | -0.9941850 | -1.0048266 | -1.0133779 | -1.0199353 | -1.0245829 | -1.0273944 | -1.0284341 | -1.0277572 | -1.0254112 | -1.0214366 | -1.0158672 | -1.0087311 | -1.0000509 | -0.9898446 | -0.9781257 | -0.9649038 | -0.9501853 | -0.9339731 | -0.9162676 | -0.8970671 | -0.8763675 | -0.8541634 | -0.8304482 | -0.8052142 | -0.7784534 | -0.7501577 | -0.7203190 | -0.6889303 | -0.6559853 | -0.6214796 | -0.5854105 | -0.5477779 | -0.5085844 | -0.4678364 | -0.4255439 | -0.3817216 | -0.3363889 | -0.2895711 | -0.2412994 | -0.1916118 | -0.1405536 |
| Gli2 | 2.1082610 | 2.0598239 | 2.0116998 | 1.9637939 | 1.9160147 | 1.8682738 | 1.8204861 | 1.7725695 | 1.7244449 | 1.6760368 | 1.6272724 | 1.5780827 | 1.5284016 | 1.4781667 | 1.4273186 | 1.3758021 | 1.3235650 | 1.2705591 | 1.2167399 | 1.1620670 | 1.1065037 | 1.0500174 | 0.9925798 | 0.9341668 | 0.8747891 | 0.8146074 | 0.7538216 | 0.6926234 | 0.6311961 | 0.5697145 | 0.5083448 | 0.4472447 | 0.3865632 | 0.3264409 | 0.2670100 | 0.2083948 | 0.1507114 | 0.0940686 | 0.0385679 | -0.0156962 | -0.0686357 | -0.1201688 | -0.1702192 | -0.2187163 | -0.2655940 | -0.3107908 | -0.3542491 | -0.3959147 | -0.4357365 | -0.4736660 | -0.5096563 | -0.5436624 | -0.5756484 | -0.6056587 | -0.6337802 | -0.6600952 | -0.6846817 | -0.7076133 | -0.7289597 | -0.7487871 | -0.7671580 | -0.7841320 | -0.7997657 | -0.8141130 | -0.8272253 | -0.8391518 | -0.8499393 | -0.8596330 | -0.8682760 | -0.8759099 | -0.8825746 | -0.8883089 | -0.8931501 | -0.8971345 | -0.9002972 | -0.9026725 | -0.9042938 | -0.9051939 | -0.9054048 | -0.9049580 | -0.9038845 | -0.9022148 | -0.8999793 | -0.8972079 | -0.8939305 | -0.8901765 | -0.8859757 | -0.8813575 | -0.8763513 | -0.8709869 | -0.8652939 | -0.8593020 | -0.8530414 | -0.8465422 | -0.8398348 | -0.8329500 | -0.8259187 | -0.8187723 | -0.8115423 | -0.8042608 |
| Dbp | 2.2506833 | 2.1891815 | 2.1281030 | 2.0673983 | 2.0070196 | 1.9469207 | 1.8870565 | 1.8273835 | 1.7678598 | 1.7084447 | 1.6490989 | 1.5897846 | 1.5304656 | 1.4711068 | 1.4116749 | 1.3521377 | 1.2924647 | 1.2326267 | 1.1725962 | 1.1123470 | 1.0518544 | 0.9910954 | 0.9300483 | 0.8686932 | 0.8070328 | 0.7451737 | 0.6832502 | 0.6213917 | 0.5597230 | 0.4983641 | 0.4374302 | 0.3770316 | 0.3172743 | 0.2582593 | 0.2000835 | 0.1428392 | 0.0866146 | 0.0314940 | -0.0224424 | -0.0751179 | -0.1264593 | -0.1763968 | -0.2248633 | -0.2717947 | -0.3171295 | -0.3608083 | -0.4027738 | -0.4429703 | -0.4813437 | -0.5178410 | -0.5524101 | -0.5849992 | -0.6155648 | -0.6441384 | -0.6707923 | -0.6955962 | -0.7186165 | -0.7399168 | -0.7595578 | -0.7775980 | -0.7940931 | -0.8090970 | -0.8226612 | -0.8348355 | -0.8456677 | -0.8552042 | -0.8634898 | -0.8705677 | -0.8764801 | -0.8812678 | -0.8849706 | -0.8876273 | -0.8892760 | -0.8899536 | -0.8896966 | -0.8885408 | -0.8865214 | -0.8836732 | -0.8800305 | -0.8756274 | -0.8704975 | -0.8646744 | -0.8581915 | -0.8510820 | -0.8433792 | -0.8351162 | -0.8263265 | -0.8170433 | -0.8073002 | -0.7971309 | -0.7865694 | -0.7756497 | -0.7644063 | -0.7528740 | -0.7410879 | -0.7290834 | -0.7168963 | -0.7045628 | -0.6921196 | -0.6796035 |
| Nr1d1 | 2.3092053 | 2.2408024 | 2.1731343 | 2.1061427 | 2.0397718 | 1.9739678 | 1.9086797 | 1.8438586 | 1.7794577 | 1.7154328 | 1.6517416 | 1.5883440 | 1.5252022 | 1.4622803 | 1.3995448 | 1.3369640 | 1.2745085 | 1.2121508 | 1.1498655 | 1.0876292 | 1.0254207 | 0.9632207 | 0.9010118 | 0.8387788 | 0.7765290 | 0.7143707 | 0.6524368 | 0.5908536 | 0.5297403 | 0.4692096 | 0.4093671 | 0.3503124 | 0.2921385 | 0.2349323 | 0.1787748 | 0.1237415 | 0.0699023 | 0.0173224 | -0.0339383 | -0.0838239 | -0.1322831 | -0.1792682 | -0.2247351 | -0.2686429 | -0.3109537 | -0.3516319 | -0.3906443 | -0.4279594 | -0.4635472 | -0.4973791 | -0.5294269 | -0.5596634 | -0.5880675 | -0.6146823 | -0.6395842 | -0.6628461 | -0.6845366 | -0.7047210 | -0.7234609 | -0.7408148 | -0.7568385 | -0.7715848 | -0.7851040 | -0.7974441 | -0.8086510 | -0.8187686 | -0.8278388 | -0.8359019 | -0.8429966 | -0.8491602 | -0.8544286 | -0.8588367 | -0.8624181 | -0.8652054 | -0.8672306 | -0.8685245 | -0.8691175 | -0.8690393 | -0.8683189 | -0.8669851 | -0.8650661 | -0.8625898 | -0.8595839 | -0.8560759 | -0.8520931 | -0.8476627 | -0.8428120 | -0.8375679 | -0.8319580 | -0.8260094 | -0.8197496 | -0.8132062 | -0.8064072 | -0.7993805 | -0.7921546 | -0.7847579 | -0.7772194 | -0.7695683 | -0.7618342 | -0.7540471 |
| Klf9 | 2.3396649 | 2.2689335 | 2.1988336 | 2.1293311 | 2.0603931 | 1.9919880 | 1.9240851 | 1.8566550 | 1.7896695 | 1.7231015 | 1.6569250 | 1.5911152 | 1.5256486 | 1.4605025 | 1.3956556 | 1.3310877 | 1.2667796 | 1.2027135 | 1.1388725 | 1.0752409 | 1.0118042 | 0.9485490 | 0.8854630 | 0.8225352 | 0.7597726 | 0.6972650 | 0.6351234 | 0.5734536 | 0.5123565 | 0.4519277 | 0.3922583 | 0.3334340 | 0.2755362 | 0.2186412 | 0.1628212 | 0.1081437 | 0.0546721 | 0.0024661 | -0.0484189 | -0.0979307 | -0.1460206 | -0.1926431 | -0.2377554 | -0.2813175 | -0.3232916 | -0.3636422 | -0.4023354 | -0.4393390 | -0.4746221 | -0.5081546 | -0.5399072 | -0.5698508 | -0.5979629 | -0.6242823 | -0.6488806 | -0.6718261 | -0.6931839 | -0.7130159 | -0.7313808 | -0.7483349 | -0.7639317 | -0.7782223 | -0.7912557 | -0.8030786 | -0.8137360 | -0.8232708 | -0.8317245 | -0.8391370 | -0.8455466 | -0.8509906 | -0.8555050 | -0.8591245 | -0.8618831 | -0.8638138 | -0.8649487 | -0.8653193 | -0.8649566 | -0.8638908 | -0.8621516 | -0.8597687 | -0.8567709 | -0.8531871 | -0.8490459 | -0.8443758 | -0.8392050 | -0.8335618 | -0.8274747 | -0.8209718 | -0.8140815 | -0.8068326 | -0.7992536 | -0.7913736 | -0.7832216 | -0.7748272 | -0.7662199 | -0.7574299 | -0.7484875 | -0.7394233 | -0.7302685 | -0.7210545 |
| Hif3a | 3.0000000 | 3.0000000 | 2.9336435 | 2.6986453 | 2.4776628 | 2.2702153 | 2.0757922 | 1.8938623 | 1.7238819 | 1.5653023 | 1.4175756 | 1.2801608 | 1.1525278 | 1.0341617 | 0.9245657 | 0.8232639 | 0.7298032 | 0.6437549 | 0.5647163 | 0.4923111 | 0.4261906 | 0.3660339 | 0.3115483 | 0.2624699 | 0.2185153 | 0.1792038 | 0.1440418 | 0.1125895 | 0.0844536 | 0.0592799 | 0.0367478 | 0.0165649 | -0.0015370 | -0.0178060 | -0.0324726 | -0.0457533 | -0.0578520 | -0.0689625 | -0.0792700 | -0.0889519 | -0.0981797 | -0.1071188 | -0.1159298 | -0.1247683 | -0.1337850 | -0.1431259 | -0.1529316 | -0.1633370 | -0.1744705 | -0.1864533 | -0.1993982 | -0.2134088 | -0.2285682 | -0.2448497 | -0.2621653 | -0.2804255 | -0.2995401 | -0.3194188 | -0.3399725 | -0.3611127 | -0.3827530 | -0.4048088 | -0.4271983 | -0.4498425 | -0.4726653 | -0.4955945 | -0.5185611 | -0.5415003 | -0.5643511 | -0.5870564 | -0.6095635 | -0.6318236 | -0.6537921 | -0.6754284 | -0.6966960 | -0.7175624 | -0.7379985 | -0.7579794 | -0.7774834 | -0.7964921 | -0.8149906 | -0.8329668 | -0.8504115 | -0.8673183 | -0.8836829 | -0.8995038 | -0.9147811 | -0.9295173 | -0.9437163 | -0.9573838 | -0.9705267 | -0.9831534 | -0.9952731 | -1.0068963 | -1.0180341 | -1.0286983 | -1.0389015 | -1.0486564 | -1.0579765 | -1.0668751 |
| Zscan2 | 3.0000000 | 3.0000000 | 3.0000000 | 2.8234181 | 2.6129709 | 2.4114810 | 2.2188710 | 2.0350363 | 1.8598491 | 1.6931620 | 1.5348124 | 1.3846251 | 1.2424161 | 1.1079953 | 0.9811692 | 0.8617433 | 0.7495248 | 0.6443243 | 0.5459577 | 0.4542485 | 0.3690287 | 0.2901413 | 0.2174407 | 0.1507952 | 0.0900368 | 0.0347738 | -0.0154221 | -0.0609420 | -0.1021442 | -0.1393576 | -0.1728857 | -0.2030092 | -0.2299894 | -0.2540697 | -0.2754788 | -0.2944317 | -0.3111324 | -0.3257748 | -0.3385442 | -0.3496189 | -0.3591711 | -0.3673677 | -0.3743715 | -0.3803420 | -0.3854358 | -0.3898072 | -0.3936091 | -0.3969926 | -0.4001082 | -0.4031053 | -0.4061325 | -0.4093379 | -0.4128594 | -0.4167416 | -0.4209756 | -0.4255520 | -0.4304610 | -0.4356929 | -0.4412381 | -0.4470866 | -0.4532286 | -0.4596542 | -0.4663535 | -0.4733166 | -0.4805335 | -0.4879943 | -0.4956893 | -0.5036084 | -0.5117418 | -0.5200798 | -0.5286126 | -0.5373306 | -0.5462241 | -0.5552835 | -0.5644995 | -0.5738626 | -0.5833635 | -0.5929930 | -0.6027420 | -0.6126015 | -0.6225627 | -0.6326166 | -0.6427547 | -0.6529683 | -0.6632491 | -0.6735888 | -0.6839790 | -0.6944119 | -0.7048793 | -0.7153736 | -0.7258870 | -0.7364121 | -0.7469413 | -0.7574674 | -0.7679833 | -0.7784819 | -0.7889564 | -0.7993999 | -0.8098059 | -0.8201679 |
| D3Ertd254e | 2.6057166 | 2.4949461 | 2.3858907 | 2.2786514 | 2.1733226 | 2.0699916 | 1.9687397 | 1.8696416 | 1.7727668 | 1.6781788 | 1.5859362 | 1.4960929 | 1.4086979 | 1.3237964 | 1.2414296 | 1.1616353 | 1.0844481 | 1.0099001 | 0.9380205 | 0.8688367 | 0.8023743 | 0.7386576 | 0.6777097 | 0.6195530 | 0.5641859 | 0.5114928 | 0.4613285 | 0.4135543 | 0.3680374 | 0.3246505 | 0.2832716 | 0.2437830 | 0.2060718 | 0.1700290 | 0.1355494 | 0.1025312 | 0.0708761 | 0.0404887 | 0.0112762 | -0.0168514 | -0.0439816 | -0.0701999 | -0.0955894 | -0.1202316 | -0.1442059 | -0.1675900 | -0.1904600 | -0.2128905 | -0.2349546 | -0.2567240 | -0.2782688 | -0.2996582 | -0.3209558 | -0.3421842 | -0.3633430 | -0.3844315 | -0.4054489 | -0.4263945 | -0.4472676 | -0.4680676 | -0.4887939 | -0.5094457 | -0.5300226 | -0.5505237 | -0.5709486 | -0.5912968 | -0.6115675 | -0.6317603 | -0.6518746 | -0.6719099 | -0.6918657 | -0.7117415 | -0.7315369 | -0.7512513 | -0.7708843 | -0.7904354 | -0.8099043 | -0.8292905 | -0.8485935 | -0.8678132 | -0.8869489 | -0.9060005 | -0.9249674 | -0.9438495 | -0.9626463 | -0.9813576 | -0.9999830 | -1.0185223 | -1.0369752 | -1.0553413 | -1.0736205 | -1.0918125 | -1.1099171 | -1.1279340 | -1.1458630 | -1.1637040 | -1.1814567 | -1.1991210 | -1.2166966 | -1.2341835 |
| Ppara | 2.7908849 | 2.6361951 | 2.4865194 | 2.3419331 | 2.2024874 | 2.0682113 | 1.9391147 | 1.8151896 | 1.6964129 | 1.5827483 | 1.4741479 | 1.3705544 | 1.2719029 | 1.1781222 | 1.0891367 | 1.0048678 | 0.9252352 | 0.8501580 | 0.7795566 | 0.7133531 | 0.6514729 | 0.5938455 | 0.5404057 | 0.4910944 | 0.4458174 | 0.4042874 | 0.3661794 | 0.3311921 | 0.2990457 | 0.2694788 | 0.2422467 | 0.2171188 | 0.1938772 | 0.1723149 | 0.1522347 | 0.1334477 | 0.1157724 | 0.0990342 | 0.0830639 | 0.0676978 | 0.0527767 | 0.0381460 | 0.0236551 | 0.0091574 | -0.0054898 | -0.0204253 | -0.0357835 | -0.0516947 | -0.0682844 | -0.0856731 | -0.1039756 | -0.1233010 | -0.1437416 | -0.1652873 | -0.1878703 | -0.2114219 | -0.2358735 | -0.2611563 | -0.2872023 | -0.3139440 | -0.3413145 | -0.3692484 | -0.3976811 | -0.4265498 | -0.4557928 | -0.4853505 | -0.5151649 | -0.5451798 | -0.5753414 | -0.6055975 | -0.6358985 | -0.6661965 | -0.6964464 | -0.7266050 | -0.7566313 | -0.7864870 | -0.8161357 | -0.8455435 | -0.8746787 | -0.9035116 | -0.9320150 | -0.9601637 | -0.9879346 | -1.0153065 | -1.0422604 | -1.0687791 | -1.0948472 | -1.1204511 | -1.1455790 | -1.1702206 | -1.1943671 | -1.2180115 | -1.2411477 | -1.2637715 | -1.2858795 | -1.3074696 | -1.3285410 | -1.3490936 | -1.3691285 | -1.3886477 |
| D130040H23Rik | 2.1775048 | 2.1049651 | 2.0337824 | 1.9639387 | 1.8954158 | 1.8281954 | 1.7622593 | 1.6975892 | 1.6341669 | 1.5719740 | 1.5109923 | 1.4512036 | 1.3925896 | 1.3351323 | 1.2788136 | 1.2236154 | 1.1695199 | 1.1165093 | 1.0645659 | 1.0136720 | 0.9638104 | 0.9149635 | 0.8671142 | 0.8202455 | 0.7743355 | 0.7293391 | 0.6852062 | 0.6418896 | 0.5993445 | 0.5575284 | 0.5164015 | 0.4759259 | 0.4360661 | 0.3967887 | 0.3580622 | 0.3198571 | 0.2821459 | 0.2449026 | 0.2081034 | 0.1717258 | 0.1357493 | 0.1001548 | 0.0649247 | 0.0300432 | -0.0045042 | -0.0387307 | -0.0726480 | -0.1062663 | -0.1395948 | -0.1726411 | -0.2054120 | -0.2379126 | -0.2701457 | -0.3020965 | -0.3337418 | -0.3650597 | -0.3960298 | -0.4266331 | -0.4568519 | -0.4866702 | -0.5160729 | -0.5450465 | -0.5735787 | -0.6016586 | -0.6292761 | -0.6564227 | -0.6830908 | -0.7092739 | -0.7349667 | -0.7601645 | -0.7848641 | -0.8090627 | -0.8327588 | -0.8559514 | -0.8786406 | -0.9008268 | -0.9225116 | -0.9436968 | -0.9643853 | -0.9845801 | -1.0042851 | -1.0235046 | -1.0422432 | -1.0605062 | -1.0782991 | -1.0956278 | -1.1124987 | -1.1289182 | -1.1448933 | -1.1604309 | -1.1755384 | -1.1902232 | -1.2044931 | -1.2183556 | -1.2318189 | -1.2448908 | -1.2575794 | -1.2698928 | -1.2818392 | -1.2934267 |
| Otx1 | 2.0888985 | 2.0292717 | 1.9703747 | 1.9121830 | 1.8546731 | 1.7978223 | 1.7416087 | 1.6860114 | 1.6310102 | 1.5765855 | 1.5227188 | 1.4693921 | 1.4165882 | 1.3642907 | 1.3124836 | 1.2611519 | 1.2102811 | 1.1598575 | 1.1098677 | 1.0602992 | 1.0111401 | 0.9623789 | 0.9140049 | 0.8660078 | 0.8183824 | 0.7711454 | 0.7243192 | 0.6779247 | 0.6319820 | 0.5865096 | 0.5415251 | 0.4970448 | 0.4530842 | 0.4096574 | 0.3667775 | 0.3244569 | 0.2827068 | 0.2415373 | 0.2009580 | 0.1609772 | 0.1216027 | 0.0828414 | 0.0446993 | 0.0071818 | -0.0297064 | -0.0659613 | -0.1015797 | -0.1365588 | -0.1708963 | -0.2045907 | -0.2376408 | -0.2700460 | -0.3018073 | -0.3329368 | -0.3634525 | -0.3933721 | -0.4227126 | -0.4514905 | -0.4797218 | -0.5074221 | -0.5346062 | -0.5612889 | -0.5874842 | -0.6132059 | -0.6384671 | -0.6632808 | -0.6876595 | -0.7116152 | -0.7351597 | -0.7583045 | -0.7810605 | -0.8034386 | -0.8254491 | -0.8471021 | -0.8684074 | -0.8893745 | -0.9100128 | -0.9303311 | -0.9503382 | -0.9700424 | -0.9894521 | -1.0085752 | -1.0274193 | -1.0459921 | -1.0643008 | -1.0823524 | -1.1001539 | -1.1177119 | -1.1350328 | -1.1521231 | -1.1689887 | -1.1856357 | -1.2020697 | -1.2182963 | -1.2343209 | -1.2501489 | -1.2657853 | -1.2812351 | -1.2965030 | -1.3115938 |
write.table(heatmap_matrix_q_value_0.01, file = file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6-significant_transcription_factors_diff_test_analysis_qval_0.01_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
# Genes of interest.
genes_of_interest <- c("Aqp4", "Fabp7", "Kif9", "Mbp", "Nes", "Pdgfra", "Top2a")
# Remove genes of interest not present in Seurat dataset
genes_not_present <- genes_of_interest[!genes_of_interest %in% rownames(seurat@data)]
genes_of_interest <- genes_of_interest[!genes_of_interest %in% genes_not_present]
if(length(genes_not_present != 0)) {
print(paste0("The following genes were not present in the Seurat object", genes_not_present))
}
diff_test_res <- differentialGeneTest(monocle[genes_of_interest],
fullModelFormulaStr = "~sm.ns(Pseudotime)")
sig_gene_names <- row.names(subset(diff_test_res, qval < 0.1))
plot_pseudotime_heatmap(monocle[genes_of_interest,],
num_clusters = 1,
cores = 1,
show_rownames = T)
p <- plot_genes_in_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
p <- p %>% remove_geom("point")
p <- p %>% remove_geom("Line")
p <- p %>% + geom_line(aes(x = Pseudotime, y = expectation), size=1)
show(p)
p <- plot_genes_branched_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
show(p)
p <- p %>% remove_geom("point")
show(p)
p <- cytokit::tsne(seurat, label=FALSE)
show(p)
p <- tsne_plot_clusters_highlighted(seurat, selected_clusters, legend=TRUE)
show(p)
p <- p + theme(legend.position = "none")
show(p)
p <- tsne_plot_clusters_highlighted_with_pseudotime(seurat, monocle, selected_clusters, legend=TRUE)
show(p)
p <- p + theme(legend.position = "none")
show(p)
save(monocle, file=file.path(monocle_objects_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6.Rda"))
cells_pseudotime <- pData(monocle) %>% select(cell, Pseudotime) %>% rename(pseudotime=Pseudotime)
write.table(cells_pseudotime, file.path(tables_directory, "2-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_cell_pseudotime.txt"), sep="\t", quote=FALSE, row.names=FALSE)
sessionInfo()
## R version 3.5.0 (2018-04-23)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS/LAPACK: /var/chroots/hydraex-centos-7/usr/lib64/R/lib/libRblas.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] splines stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] viridis_0.5.1 viridisLite_0.3.0 forcats_0.4.0
## [4] stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.0
## [7] tidyr_0.8.2 tibble_2.0.1 tidyverse_1.2.1
## [10] Seurat_2.3.4 cowplot_0.9.4 R.utils_2.8.0
## [13] R.oo_1.22.0 R.methodsS3_1.7.1 readr_1.3.1
## [16] readxl_1.3.0 patchwork_0.0.1 monocle_2.10.1
## [19] DDRTree_0.1.5 irlba_2.3.3 VGAM_1.1-1
## [22] Biobase_2.42.0 BiocGenerics_0.28.0 Matrix_1.2-15
## [25] kableExtra_1.0.1 ggedit_0.3.0 ggplot2_3.1.0
## [28] cytokit_0.6.0 pheatmap_1.0.12 colorRamps_2.3
##
## loaded via a namespace (and not attached):
## [1] snow_0.4-3 backports_1.1.3 Hmisc_4.2-0
## [4] plyr_1.8.4 igraph_1.2.4 lazyeval_0.2.1
## [7] densityClust_0.3 fastICA_1.2-1 digest_0.6.18
## [10] foreach_1.4.4 htmltools_0.3.6 lars_1.2
## [13] gdata_2.18.0 magrittr_1.5 checkmate_1.9.1
## [16] cluster_2.0.7-1 mixtools_1.1.0 ROCR_1.0-7
## [19] limma_3.38.3 modelr_0.1.3 matrixStats_0.54.0
## [22] docopt_0.6.1 colorspace_1.4-0 ggrepel_0.8.0
## [25] rvest_0.3.2 haven_2.0.0 xfun_0.4
## [28] sparsesvd_0.1-4 crayon_1.3.4 jsonlite_1.6
## [31] survival_2.43-3 zoo_1.8-4 iterators_1.0.10
## [34] ape_5.2 glue_1.3.0 gtable_0.2.0
## [37] webshot_0.5.1 kernlab_0.9-27 prabclus_2.2-7
## [40] DEoptimR_1.0-8 scales_1.0.0 mvtnorm_1.0-8
## [43] bibtex_0.4.2 miniUI_0.1.1.1 Rcpp_1.0.0
## [46] metap_1.1 dtw_1.20-1 xtable_1.8-3
## [49] htmlTable_1.13.1 reticulate_1.11.1 foreign_0.8-71
## [52] bit_1.1-14 proxy_0.4-22 mclust_5.4.2
## [55] SDMTools_1.1-221 Formula_1.2-3 tsne_0.1-3
## [58] htmlwidgets_1.3 httr_1.4.0 FNN_1.1.3
## [61] gplots_3.0.1.1 RColorBrewer_1.1-2 shinyAce_0.3.3
## [64] fpc_2.1-11.1 acepack_1.4.1 modeltools_0.2-22
## [67] ica_1.0-2 pkgconfig_2.0.2 flexmix_2.3-14
## [70] nnet_7.3-12 labeling_0.3 tidyselect_0.2.5
## [73] rlang_0.3.1 reshape2_1.4.3 later_0.8.0
## [76] cellranger_1.1.0 munsell_0.5.0 tools_3.5.0
## [79] cli_1.0.1 generics_0.0.2 broom_0.5.1
## [82] ggridges_0.5.1 evaluate_0.13 shinyBS_0.61
## [85] yaml_2.2.0 npsurv_0.4-0 knitr_1.21
## [88] bit64_0.9-7 fitdistrplus_1.0-14 robustbase_0.93-3
## [91] caTools_1.17.1.1 randomForest_4.6-14 RANN_2.6.1
## [94] pbapply_1.4-0 nlme_3.1-137 mime_0.6
## [97] slam_0.1-44 xml2_1.2.0 hdf5r_1.0.0
## [100] compiler_3.5.0 rstudioapi_0.9.0 png_0.1-7
## [103] lsei_1.2-0 stringi_1.3.1 highr_0.7
## [106] lattice_0.20-35 trimcluster_0.1-2.1 HSMMSingleCell_1.2.0
## [109] pillar_1.3.1 combinat_0.0-8 Rdpack_0.10-1
## [112] lmtest_0.9-36 data.table_1.12.0 bitops_1.0-6
## [115] gbRd_0.4-11 httpuv_1.4.5.1 R6_2.4.0
## [118] latticeExtra_0.6-28 promises_1.0.1 KernSmooth_2.23-15
## [121] gridExtra_2.3 codetools_0.2-15 MASS_7.3-51.1
## [124] gtools_3.8.1 assertthat_0.2.0 withr_2.1.2
## [127] qlcMatrix_0.9.7 diptest_0.75-7 doSNOW_1.0.16
## [130] hms_0.4.2 grid_3.5.0 rpart_4.1-13
## [133] class_7.3-14 rmarkdown_1.11 segmented_0.5-3.0
## [136] Rtsne_0.15 lubridate_1.7.4 shiny_1.2.0
## [139] base64enc_0.1-3